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Diet transcriptome

Martine C Morrison, Robert Kleemann, Arianne van Koppen, Roeland Hanemaaijer, Lars Verschuren
Introduction: It is generally accepted that metabolic inflammation in the liver is an important driver of disease progression in NASH and associated matrix remodeling/fibrosis. However, the exact molecular inflammatory mechanisms are poorly defined in human studies. Investigation of key pathogenic mechanisms requires the use of pre-clinical models, for instance for time-resolved studies. Such models must reflect molecular disease processes of importance in patients. Herein we characterized inflammation in NASH patients on the molecular level by transcriptomics and investigated whether key human disease pathways can be recapitulated experimentally in Ldlr-/- ...
2018: Frontiers in Physiology
Parastoo Fazelzadeh, Roland W J Hangelbroek, Peter J Joris, Casper G Schalkwijk, Diederik Esser, Lydia Afman, Thomas Hankemeier, Doris M Jacobs, Velitchka V Mihaleva, Sander Kersten, John van Duynhoven, Mark V Boekschoten
Introduction: The response to dietary challenges has been proposed as a more accurate measure of metabolic health than static measurements performed in the fasted state. This has prompted many groups to explore the potential of dietary challenge tests for assessment of diet and lifestyle induced shifts in metabolic phenotype. Objectives: We examined whether the response to a mixed-meal challenge could provide a readout for a weight loss (WL)-induced phenotype shift in abdominally obese male subjects...
2018: Metabolomics: Official Journal of the Metabolomic Society
Carrie J Finno, Matthew H Bordbari, Giuliana Gianino, Brittni Ming-Whitfield, Erin Burns, Janel Merkel, Monica Britton, Blythe Durbin-Johnson, Erica A Sloma, Marissa McMackin, Gino Cortopassi, Victor Rivas, Marietta Barro, Cecilia K Tran, Ingrid Gennity, Hadi Habib, Libin Xu, Birgit Puschner, Andrew D Miller
Mice with deficiency in tocopherol (alpha) transfer protein gene develop peripheral tocopherol deficiency and sensory neurodegeneration. Ttpa-/- mice maintained on diets with deficient α-tocopherol (α-TOH) had proprioceptive deficits by six months of age, axonal degeneration and neuronal chromatolysis within the dorsal column of the spinal cord and its projections into the medulla. Transmission electron microscopy revealed degeneration of dorsal column axons. We addressed the potential pathomechanism of α-TOH deficient neurodegeneration by global transcriptome sequencing within the spinal cord and cerebellum...
March 8, 2018: Free Radical Biology & Medicine
Jan Perner, Jan Kotál, Tereza Hatalová, Veronika Urbanová, Pavla Bartošová-Sojková, Peter M Brophy, Petr Kopáček
Blood-feeding parasites are inadvertently exposed to high doses of potentially cytotoxic haem liberated upon host blood digestion. Detoxification of free haem is a special challenge for ticks, which digest haemoglobin intracellularly. Ticks lack a haem catabolic mechanism, mediated by haem oxygenase, and need to dispose of vast majority of acquired haem via its accumulation in haemosomes. The knowledge of individual molecules involved in the maintenance of haem homeostasis in ticks is still rather limited. RNA-seq analyses of the Ixodes ricinus midguts from blood- and serum-fed females identified an abundant transcript of glutathione S-transferase (gst) to be substantially up-regulated in the presence of red blood cells in the diet...
March 8, 2018: Insect Biochemistry and Molecular Biology
Kan Gao, Yu Pi, Chun-Long Mu, Yu Peng, Zan Huang, Wei-Yun Zhu
The evidence of gut microbiota-mediated modulation of brain function has been widely recognized from studies using germ-free rodents or animals with oral antibiotic-induced microbiota depletion. Since the number of bacteria in the large intestine greatly exceeds that found within the small intestine, large intestinal microbiota may play a crucial role in the modulation of brain function. In the present study, twelve piglets (12.08 ± 0.28 kg) fitted with a T-cannula at the distal ileum were fed a standard diet and randomly assigned to two groups (n=6) for ileal infusion of either saline (control group) or antibiotics (antibiotic group)...
March 10, 2018: Journal of Neurochemistry
Afshin Beheshti, Egle Cekanaviciute, David J Smith, Sylvain V Costes
Spaceflight introduces a combination of environmental stressors, including microgravity, ionizing radiation, changes in diet and altered atmospheric gas composition. In order to understand the impact of each environmental component on astronauts it is important to investigate potential influences in isolation. Rodent spaceflight experiments involve both standard vivarium cages and animal enclosure modules (AEMs), which are cages used to house rodents in spaceflight. Ground control AEMs are engineered to match the spaceflight environment...
March 8, 2018: Scientific Reports
Kinyui Alice Lo, Shiqi Huang, Arcinas Camille Esther Walet, Zhi-Chun Zhang, Melvin Khee-Shing Leow, Meihui Liu, Lei Sun
Obesity induces profound transcriptome changes in adipocytes; recent evidence suggests that lncRNAs play key roles in this process. Here, we performed a comprehensive transcriptome study by RNA-Seq in adipocytes isolated from interscapular brown, inguinal and epididymal white adipose tissues in diet-induced obese mice. Our analysis reveals a set of obesity-dysregulated lncRNAs, many of which exhibit dynamic changes in fed vs. fasted state, potentially serving as novel molecular markers reflecting adipose energy status...
March 8, 2018: Diabetes
Zengpeng Lv, Hao Fan, Beibei Zhang, Chao Ning, Kun Xing, Yuming Guo
Genistein (GEN) is a type of isoflavone mainly derived from soy products. In this experiment, we added 40 and 400 mg/kg GEN to the diet of laying broiler breeder hens to clarify the maternal effects of GEN on the development and metabolism of chick embryos. GEN treatment at 40 mg/kg increased embryonic length, weight, and liver index, as well as the width of the proliferative zone in the tibial growth plate of chick embryos. Gene ontology (GO) cluster analysis of the hepatic transcriptome showed that GEN treatment promoted embryonic development and cell proliferation...
March 8, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
Sobha Puppala, Cun Li, Jeremy P Glenn, Romil Saxena, Samer Gawrieh, Amy Quinn, Jennifer Palarczyk, Edward J Dick, Peter W Nathanielsz, Laura A Cox
Maternal obesity (MO) increases offspring cardiometabolic disease risk. Altered fetal liver development in response to the challenge of MO has metabolic consequences underlying adverse offspring life-course health outcomes. Little is known about molecular pathways and potential epigenetic changes regulating primate fetal liver responses to MO. We hypothesized that MO would induce fetal baboon liver epigenetic changes resulting in dysregulation of key metabolic pathways that impact lipid metabolism. MO was induced prior to pregnancy by a high fat, high sucrose diet...
March 7, 2018: Journal of Physiology
Eva Gómez-Orte, Eric Cornes, Angelina Zheleva, Beatriz Sáenz-Narciso, María de Toro, María Iñiguez, Rosario López, Juan-Félix San-Juan, Begoña Ezcurra, Begoña Sacristán, Adolfo Sánchez-Blanco, Julián Cerón, Juan Cabello
The transcriptomes of model organisms have been defined under specific laboratory growth conditions. The standard protocol for Caenorhabditis elegans growth and maintenance is 20°C on an Escherichia coli diet. Temperatures ranging from 15°C to 25°C or feeding with other species of bacteria are considered physiological conditions, but the effect of these conditions on the worm transcriptome has not been well characterized. Here, we compare the global gene expression profile for the reference Caenorhabditis elegans strain (N2) grown at 15°C, 20°C, and 25°C on two different diets, Escherichia coli and Bacillus subtilis ...
February 9, 2018: Oncotarget
C Desert, E Baéza, M Aite, M Boutin, A Le Cam, J Montfort, M Houee-Bigot, Y Blum, P F Roux, C Hennequet-Antier, C Berri, S Metayer-Coustard, A Collin, S Allais, E Le Bihan, D Causeur, F Gondret, M J Duclos, S Lagarrigue
BACKGROUND: Because the cost of cereals is unstable and represents a large part of production charges for meat-type chicken, there is an urge to formulate alternative diets from more cost-effective feedstuff. We have recently shown that meat-type chicken source is prone to adapt to dietary starch substitution with fat and fiber. The aim of this study was to better understand the molecular mechanisms of this adaptation to changes in dietary energy sources through the fine characterization of transcriptomic changes occurring in three major metabolic tissues - liver, adipose tissue and muscle - as well as in circulating blood cells...
March 7, 2018: BMC Genomics
Mark A Phuong, Gusti N Mahardika
To expand our capacity to discover venom sequences from the genomes of venomous organisms, we applied targeted sequencing techniques to selectively recover venom gene superfamilies and non-toxin loci from the genomes of 32 cone snail species (family, Conidae), a diverse group of marine gastropods that capture their prey using a cocktail of neurotoxic peptides (conotoxins). We were able to successfully recover conotoxin gene superfamilies across all species with high confidence (> 100X coverage) and used these data to provide new insights into conotoxin evolution...
March 5, 2018: Molecular Biology and Evolution
Timothy W Rhoads, Maggie S Burhans, Vincent B Chen, Paul D Hutchins, Matthew J P Rush, Josef P Clark, Jaime L Stark, Sean J McIlwain, Hamid R Eghbalnia, Derek M Pavelec, Irene M Ong, John M Denu, John L Markley, Joshua J Coon, Ricki J Colman, Rozalyn M Anderson
Caloric restriction (CR) extends lifespan and delays the onset of age-related disorders in diverse species. Metabolic regulatory pathways have been implicated in the mechanisms of CR, but the molecular details have not been elucidated. Here, we show that CR engages RNA processing of genes associated with a highly integrated reprogramming of hepatic metabolism. We conducted molecular profiling of liver biopsies collected from adult male rhesus monkeys (Macaca mulatta) at baseline and after 2 years on control or CR (30% restricted) diet...
March 6, 2018: Cell Metabolism
Zehra Omeroğlu Ulu, Salih Ulu, Soner Dogan, Bilge Guvenc Tuna, Nehir Ozdemir Ozgenturk
Calorie restriction (CR), which is a factor that expands lifespan and an important player in immune response, is an effective protective method against cancer development. Thymus, which plays a critical role in the development of the immune system, reacts to nutrition deficiency quickly. RNA-seq-based transcriptome sequencing was performed to thymus tissues of MMTV-TGF- α mice subjected to ad libitum (AL), chronic calorie restriction (CCR), and intermittent calorie restriction (ICR) diets in this study. Three cDNA libraries were sequenced using Illumina HiSeq™ 4000 to produce 100 base pair-end reads...
2018: International Journal of Genomics
Kai K Lie, Ole K Tørresen, Monica Hongrø Solbakken, Ivar Rønnestad, Ave Tooming-Klunderud, Alexander J Nederbragt, Sissel Jentoft, Øystein Sæle
BACKGROUND: The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach loss has occurred independently multiple times in the course of evolution. By assembling the ballan wrasse genome and transcriptome we aimed to determine the genetic basis for its digestive system function and appetite regulation...
March 6, 2018: BMC Genomics
Nadeeja N Wijayatunga, Mandana Pahlavani, Nishan S Kalupahana, Kameswara Rao Kottapalli, Preethi H Gunaratne, Cristian Coarfa, Latha Ramalingam, Naima Moustaid-Moussa
Obesity contributes to metabolic disorders such as diabetes and cardiovascular disease. Characterization of differences between the main adipose tissue depots, white (WAT) [including subcutaneous (SAT) and visceral adipose tissue (VAT)] and brown adipose tissue (BAT) helps to identify their roles in obesity. Thus, we studied depot-specific differences in whole transcriptome and miRNA profiles of SAT, VAT and BAT from high fat diet (HFD/45% of calories from fat) fed mice using RNA sequencing and small RNA-Seq...
February 6, 2018: Oncotarget
Zehong Wei, Huihui Zhou, Yanjiao Zhang, Qin Zhang, Wenbing Zhang, Kangsen Mai
A previous study showed that flesh quality of large yellow croaker (LYC) was improved by feeding dietary hydroxyproline (Hyp, 0·69 %). The aim of the present study was to explore the underlying mechanisms using transcriptomics and metabolomics analysis. The metabolomics analysis showed that muscle metabolite profiles could be clearly separated between the basal diet and Hyp supplementation diet. Metabolites including betaine, Hyp, lactate, glucose-6-phosphate, trimethylamine N-oxide, taurine, creatine, inosine monophosphate, histamine and serine made significant contribution to the separation...
February 2018: British Journal of Nutrition
Stephen Frenk, Jonathan Houseley
Ageing leads to dramatic changes in the physiology of many different tissues resulting in a spectrum of pathology. Nonetheless, many lines of evidence suggest that ageing is driven by highly conserved cell intrinsic processes, and a set of unifying hallmarks of ageing has been defined. Here, we survey reports of age-linked changes in basal gene expression across eukaryotes from yeast to human and identify six gene expression hallmarks of cellular ageing: downregulation of genes encoding mitochondrial proteins; downregulation of the protein synthesis machinery; dysregulation of immune system genes; reduced growth factor signalling; constitutive responses to stress and DNA damage; dysregulation of gene expression and mRNA processing...
February 28, 2018: Biogerontology
Amy J Osborne, Peter K Dearden
The Developmental Origins of Health and Disease hypothesis predicts that early-life environmental exposures can be detrimental to later-life health and that mismatch between the pre- and post-natal environment may contribute to the growing non-communicable disease epidemic. Within this is an increasingly recognized role for epigenetic mechanisms; for example, epigenetic modifications can be influenced by nutrition and can alter gene expression in mothers and offspring. Currently, there are few whole-genome transcriptional studies of response to nutritional alteration...
October 2017: Environmental Epigenetics
Mariona Pinart, Katharina Nimptsch, Jildau Bouwman, Lars O Dragsted, Chen Yang, Nathalie De Cock, Carl Lachat, Giuditta Perozzi, Raffaella Canali, Rosario Lombardo, Massimo D'Archivio, Michèle Guillaume, Anne-Françoise Donneau, Stephanie Jeran, Jakob Linseisen, Christina Kleiser, Ute Nöthlings, Janett Barbaresko, Heiner Boeing, Marta Stelmach-Mardas, Thorsten Heuer, Eamon Laird, Janette Walton, Paolo Gasparini, Antonietta Robino, Luis Castaño, Gemma Rojo-Martínez, Jordi Merino, Luis Masana, Marie Standl, Holger Schulz, Elena Biagi, Eha Nurk, Christophe Matthys, Marco Gobbetti, Maria de Angelis, Eberhard Windler, Birgit-Christiane Zyriax, Jean Tafforeau, Tobias Pischon
Background: Joint data analysis from multiple nutrition studies may improve the ability to answer complex questions regarding the role of nutritional status and diet in health and disease. Objective: The objective was to identify nutritional observational studies from partners participating in the European Nutritional Phenotype Assessment and Data Sharing Initiative (ENPADASI) Consortium, as well as minimal requirements for joint data analysis. Methods: A predefined template containing information on study design, exposure measurements (dietary intake, alcohol and tobacco consumption, physical activity, sedentary behavior, anthropometric measures, and sociodemographic and health status), main health-related outcomes, and laboratory measurements (traditional and omics biomarkers) was developed and circulated to those European research groups participating in the ENPADASI under the strategic research area of "diet-related chronic diseases...
February 1, 2018: Journal of Nutrition
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